[R] invoking R scripts from a linux shell ?

Itay Furman itayf at fhcrc.org
Fri Jan 16 06:44:13 CET 2004

On Thu, 15 Jan 2004, Enrico Curiotto wrote:

> Hello,
> I have written perl programs that extract data from a
> text file, process them, and create other text files,
> which I'd like to apply some statistics too (for
> example with R).
> I'd like to do it all in once , with a single script.
> I'm not familiar with R, I'd like to know if this task
> could be accomplished by creating a linux shells that
> launches the perl scripts and then "R functions" that
> maybe pass back some results to the system like in
> this schema:

You could call R in BATCH mode from the perl script using
one of the system interface operators, e.g., "system", or use the 
'Shell' module.

I have also bumped (but didn't try yet) into R-Perl interface 
called RSPerl which might be much more than you what you need.
I think it is under the "Omega" link in the R website. If not
google for RSPerl.

'R --help' will give you pointers to running R in BATCH mode.


itayf at fhcrc.org		Fred Hutchinson Cancer Research Center

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